Multiple sequence alignment - TraesCS2B01G587200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G587200 chr2B 100.000 3431 0 0 1 3431 773730957 773734387 0.000000e+00 6336.0
1 TraesCS2B01G587200 chr2B 91.813 342 11 2 883 1207 773078839 773078498 8.680000e-126 460.0
2 TraesCS2B01G587200 chr2B 81.727 498 47 18 2632 3110 147797791 147798263 3.230000e-100 375.0
3 TraesCS2B01G587200 chr2B 87.200 250 21 7 544 790 773082947 773082706 1.210000e-69 274.0
4 TraesCS2B01G587200 chr2B 78.689 244 48 2 3080 3323 43804010 43803771 3.540000e-35 159.0
5 TraesCS2B01G587200 chr2B 78.355 231 46 2 3093 3323 50629941 50629715 2.760000e-31 147.0
6 TraesCS2B01G587200 chr2B 77.049 244 52 2 3080 3323 50485444 50485683 1.660000e-28 137.0
7 TraesCS2B01G587200 chr2D 85.751 1972 169 53 1538 3431 630632910 630634847 0.000000e+00 1982.0
8 TraesCS2B01G587200 chr2D 86.116 1635 114 47 1548 3110 629726395 629727988 0.000000e+00 1657.0
9 TraesCS2B01G587200 chr2D 85.879 1558 116 43 1595 3085 629990508 629988988 0.000000e+00 1563.0
10 TraesCS2B01G587200 chr2D 83.127 1612 128 61 1577 3110 630090875 630089330 0.000000e+00 1338.0
11 TraesCS2B01G587200 chr2D 83.577 822 93 18 2 787 630092625 630091810 0.000000e+00 732.0
12 TraesCS2B01G587200 chr2D 80.364 1044 107 62 348 1371 629991761 629990796 0.000000e+00 702.0
13 TraesCS2B01G587200 chr2D 81.455 701 53 36 883 1535 630091724 630091053 1.420000e-138 503.0
14 TraesCS2B01G587200 chr2D 85.409 514 29 14 883 1371 630631869 630632361 3.080000e-135 492.0
15 TraesCS2B01G587200 chr2D 88.235 408 41 6 1 406 630629726 630630128 6.660000e-132 481.0
16 TraesCS2B01G587200 chr2D 84.901 404 47 10 11 406 629992145 629991748 2.480000e-106 396.0
17 TraesCS2B01G587200 chr2D 81.208 298 38 14 994 1279 30662304 30662013 1.240000e-54 224.0
18 TraesCS2B01G587200 chr2D 78.367 245 48 3 3080 3323 30659637 30659397 1.650000e-33 154.0
19 TraesCS2B01G587200 chr2D 80.693 202 18 6 2900 3100 630049711 630049530 1.660000e-28 137.0
20 TraesCS2B01G587200 chr2D 81.481 81 5 5 799 869 630631630 630631710 1.330000e-04 58.4
21 TraesCS2B01G587200 chr2D 100.000 30 0 0 1548 1577 630632538 630632567 4.780000e-04 56.5
22 TraesCS2B01G587200 chr2A 88.163 980 62 20 1867 2801 760772006 760772976 0.000000e+00 1118.0
23 TraesCS2B01G587200 chr2A 88.502 948 56 23 1867 2768 760508799 760507859 0.000000e+00 1098.0
24 TraesCS2B01G587200 chr2A 87.050 834 55 17 1865 2650 760490411 760489583 0.000000e+00 893.0
25 TraesCS2B01G587200 chr2A 90.408 490 21 13 895 1371 760770800 760771276 3.760000e-174 621.0
26 TraesCS2B01G587200 chr2A 93.956 364 22 0 3067 3430 760507176 760506813 5.000000e-153 551.0
27 TraesCS2B01G587200 chr2A 91.525 295 14 6 1078 1371 760509435 760509151 2.480000e-106 396.0
28 TraesCS2B01G587200 chr2A 83.082 331 38 9 2647 2962 760478652 760478325 5.600000e-73 285.0
29 TraesCS2B01G587200 chr2A 88.889 153 13 3 2760 2912 760507464 760507316 5.850000e-43 185.0
30 TraesCS2B01G587200 chr2A 88.976 127 14 0 2984 3110 760477036 760476910 1.270000e-34 158.0
31 TraesCS2B01G587200 chr2A 78.319 226 41 4 3103 3323 33005358 33005580 4.620000e-29 139.0
32 TraesCS2B01G587200 chr2A 84.746 118 16 2 2655 2770 33021180 33021297 2.160000e-22 117.0
33 TraesCS2B01G587200 chr2A 93.590 78 4 1 2979 3056 760507291 760507215 7.780000e-22 115.0
34 TraesCS2B01G587200 chr2A 80.137 146 27 1 3178 3323 32919938 32919795 1.300000e-19 108.0
35 TraesCS2B01G587200 chr2A 84.404 109 12 5 2667 2770 32920939 32920831 6.060000e-18 102.0
36 TraesCS2B01G587200 chr2A 83.036 112 17 1 3219 3330 33022187 33022296 2.180000e-17 100.0
37 TraesCS2B01G587200 chr2A 94.737 57 2 1 994 1049 760509496 760509440 1.700000e-13 87.9
38 TraesCS2B01G587200 chr2A 96.078 51 2 0 3321 3371 760773610 760773660 2.190000e-12 84.2
39 TraesCS2B01G587200 chr2A 92.000 50 3 1 3382 3430 760773692 760773741 6.140000e-08 69.4
40 TraesCS2B01G587200 chr2A 97.297 37 1 0 1541 1577 760509004 760508968 2.860000e-06 63.9
41 TraesCS2B01G587200 chr2A 100.000 30 0 0 1548 1577 760771454 760771483 4.780000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G587200 chr2B 773730957 773734387 3430 False 6336.000000 6336 100.000000 1 3431 1 chr2B.!!$F3 3430
1 TraesCS2B01G587200 chr2B 773078498 773082947 4449 True 367.000000 460 89.506500 544 1207 2 chr2B.!!$R3 663
2 TraesCS2B01G587200 chr2D 629726395 629727988 1593 False 1657.000000 1657 86.116000 1548 3110 1 chr2D.!!$F1 1562
3 TraesCS2B01G587200 chr2D 629988988 629992145 3157 True 887.000000 1563 83.714667 11 3085 3 chr2D.!!$R3 3074
4 TraesCS2B01G587200 chr2D 630089330 630092625 3295 True 857.666667 1338 82.719667 2 3110 3 chr2D.!!$R4 3108
5 TraesCS2B01G587200 chr2D 630629726 630634847 5121 False 613.980000 1982 88.175200 1 3431 5 chr2D.!!$F2 3430
6 TraesCS2B01G587200 chr2A 760489583 760490411 828 True 893.000000 893 87.050000 1865 2650 1 chr2A.!!$R1 785
7 TraesCS2B01G587200 chr2A 760770800 760773741 2941 False 389.820000 1118 93.329800 895 3430 5 chr2A.!!$F3 2535
8 TraesCS2B01G587200 chr2A 760506813 760509496 2683 True 356.685714 1098 92.642286 994 3430 7 chr2A.!!$R4 2436
9 TraesCS2B01G587200 chr2A 760476910 760478652 1742 True 221.500000 285 86.029000 2647 3110 2 chr2A.!!$R3 463

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
880 5856 0.614979 GCAGACCCAGGGTAGACTCA 60.615 60.0 12.69 0.0 35.25 3.41 F
1387 6603 0.179020 TCAGAACAAGTGCCCTGTGG 60.179 55.0 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 8502 0.251474 AGCTCAAGAAAGCCATGGCA 60.251 50.0 37.18 14.88 43.56 4.92 R
3265 11213 0.037326 GCCCTTGCTTTTACCTTGCC 60.037 55.0 0.00 0.00 33.53 4.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 6.024664 TCAATATACGGCGAACATTTTTGTG 58.975 36.000 16.62 0.00 0.00 3.33
61 66 9.790344 TTTTTGTGGGTCATGATGAATATTTTT 57.210 25.926 0.00 0.00 0.00 1.94
114 119 9.425577 TGTGATAGACATTTTTAATACACGACA 57.574 29.630 0.00 0.00 0.00 4.35
132 137 8.415192 ACACGACAATCATACGTTAATACATT 57.585 30.769 0.00 0.00 38.18 2.71
133 138 8.325282 ACACGACAATCATACGTTAATACATTG 58.675 33.333 0.00 0.00 38.18 2.82
190 197 6.084326 ACATGTGGGACTTTTTAACACATC 57.916 37.500 0.00 0.00 46.42 3.06
342 355 7.683676 CGCAACAAGATTTTATTTCCGAAAATG 59.316 33.333 0.00 0.00 36.78 2.32
343 356 7.956943 GCAACAAGATTTTATTTCCGAAAATGG 59.043 33.333 0.00 0.00 36.78 3.16
345 358 9.942850 AACAAGATTTTATTTCCGAAAATGGAT 57.057 25.926 0.00 0.00 36.78 3.41
459 517 9.195411 ACAATATTTGAAAAATGTGCACAGTAG 57.805 29.630 25.84 4.41 0.00 2.57
460 518 8.649841 CAATATTTGAAAAATGTGCACAGTAGG 58.350 33.333 25.84 0.00 0.00 3.18
463 521 3.382865 TGAAAAATGTGCACAGTAGGCAA 59.617 39.130 25.84 5.65 43.91 4.52
465 523 3.581024 AAATGTGCACAGTAGGCAATG 57.419 42.857 25.84 0.00 43.91 2.82
481 539 6.160576 AGGCAATGTTTGAACTGTACAATT 57.839 33.333 0.00 0.00 0.00 2.32
578 639 3.705043 ATCGGCTAAACGTAACGATCT 57.295 42.857 0.00 0.00 39.81 2.75
581 642 3.065786 TCGGCTAAACGTAACGATCTGAT 59.934 43.478 0.00 0.00 34.94 2.90
582 643 3.179795 CGGCTAAACGTAACGATCTGATG 59.820 47.826 0.00 0.00 0.00 3.07
587 648 1.202417 ACGTAACGATCTGATGGGCAG 60.202 52.381 4.67 0.00 46.31 4.85
609 670 4.950475 AGAGTGGATGATAAAGACGTCTCA 59.050 41.667 20.33 13.16 0.00 3.27
624 685 2.226674 CGTCTCATAGATAGCGGCTTCA 59.773 50.000 8.26 0.00 0.00 3.02
631 692 1.016627 GATAGCGGCTTCATGTTGCA 58.983 50.000 8.26 0.00 0.00 4.08
696 1909 6.183360 CGGATAGATCAAAGTGTGAAAGCATT 60.183 38.462 0.00 0.00 40.50 3.56
794 2014 3.256281 GAGGGAGCCTCTTTGGTTG 57.744 57.895 0.00 0.00 46.41 3.77
797 2017 0.895559 GGGAGCCTCTTTGGTTGTGG 60.896 60.000 0.00 0.00 38.35 4.17
801 5762 1.179174 GCCTCTTTGGTTGTGGGGTC 61.179 60.000 0.00 0.00 38.35 4.46
872 5848 4.704833 CCACGTGCAGACCCAGGG 62.705 72.222 10.91 2.85 0.00 4.45
873 5849 3.941188 CACGTGCAGACCCAGGGT 61.941 66.667 12.53 12.53 39.44 4.34
877 5853 1.597461 GTGCAGACCCAGGGTAGAC 59.403 63.158 12.69 4.01 35.25 2.59
880 5856 0.614979 GCAGACCCAGGGTAGACTCA 60.615 60.000 12.69 0.00 35.25 3.41
881 5857 1.479709 CAGACCCAGGGTAGACTCAG 58.520 60.000 12.69 0.00 35.25 3.35
1288 6491 1.087501 GTGCGTCCTCCAATCCTTTC 58.912 55.000 0.00 0.00 0.00 2.62
1290 6493 0.253327 GCGTCCTCCAATCCTTTCCT 59.747 55.000 0.00 0.00 0.00 3.36
1291 6494 1.340114 GCGTCCTCCAATCCTTTCCTT 60.340 52.381 0.00 0.00 0.00 3.36
1292 6495 2.633488 CGTCCTCCAATCCTTTCCTTC 58.367 52.381 0.00 0.00 0.00 3.46
1294 6497 3.307762 CGTCCTCCAATCCTTTCCTTCTT 60.308 47.826 0.00 0.00 0.00 2.52
1295 6498 4.013050 GTCCTCCAATCCTTTCCTTCTTG 58.987 47.826 0.00 0.00 0.00 3.02
1296 6499 3.010584 TCCTCCAATCCTTTCCTTCTTGG 59.989 47.826 0.00 0.00 38.14 3.61
1297 6500 3.010584 CCTCCAATCCTTTCCTTCTTGGA 59.989 47.826 0.00 0.00 42.22 3.53
1298 6501 4.325658 CCTCCAATCCTTTCCTTCTTGGAT 60.326 45.833 3.03 0.00 45.68 3.41
1299 6502 4.603131 TCCAATCCTTTCCTTCTTGGATG 58.397 43.478 0.00 0.00 45.68 3.51
1300 6503 3.703052 CCAATCCTTTCCTTCTTGGATGG 59.297 47.826 0.00 0.00 45.68 3.51
1301 6504 4.570505 CCAATCCTTTCCTTCTTGGATGGA 60.571 45.833 0.00 8.57 45.68 3.41
1339 6542 2.379459 GCCCCCTTCTTCTCCCCTC 61.379 68.421 0.00 0.00 0.00 4.30
1340 6543 1.694525 CCCCCTTCTTCTCCCCTCC 60.695 68.421 0.00 0.00 0.00 4.30
1384 6600 2.229784 GGAATTCAGAACAAGTGCCCTG 59.770 50.000 7.93 0.00 0.00 4.45
1385 6601 2.664402 ATTCAGAACAAGTGCCCTGT 57.336 45.000 0.00 0.00 0.00 4.00
1386 6602 1.679139 TTCAGAACAAGTGCCCTGTG 58.321 50.000 0.00 0.00 0.00 3.66
1387 6603 0.179020 TCAGAACAAGTGCCCTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
1415 6631 2.293399 GCTCTGTCGTCCAACCAATTTT 59.707 45.455 0.00 0.00 0.00 1.82
1455 6686 0.694771 TCTGCCTTTGGATGACTGCT 59.305 50.000 0.00 0.00 0.00 4.24
1459 6690 1.888512 GCCTTTGGATGACTGCTTTGA 59.111 47.619 0.00 0.00 0.00 2.69
1474 6707 3.068024 TGCTTTGACCAATTTCAGTGTCC 59.932 43.478 0.00 0.00 0.00 4.02
1478 6711 2.711009 TGACCAATTTCAGTGTCCCTCT 59.289 45.455 0.00 0.00 0.00 3.69
1485 6718 0.972134 TCAGTGTCCCTCTCTGCAAG 59.028 55.000 0.00 0.00 37.51 4.01
1490 6723 2.497675 GTGTCCCTCTCTGCAAGACATA 59.502 50.000 0.00 0.00 38.67 2.29
1491 6724 3.055819 GTGTCCCTCTCTGCAAGACATAA 60.056 47.826 0.00 0.00 38.67 1.90
1492 6725 3.776969 TGTCCCTCTCTGCAAGACATAAT 59.223 43.478 0.00 0.00 38.67 1.28
1493 6726 4.962362 TGTCCCTCTCTGCAAGACATAATA 59.038 41.667 0.00 0.00 38.67 0.98
1496 6729 4.754114 CCCTCTCTGCAAGACATAATAAGC 59.246 45.833 0.00 0.00 38.67 3.09
1500 6733 6.882656 TCTCTGCAAGACATAATAAGCTTCT 58.117 36.000 0.00 0.00 38.67 2.85
1506 6739 7.708322 TGCAAGACATAATAAGCTTCTCAGTAG 59.292 37.037 0.00 0.00 0.00 2.57
1515 6748 8.854614 AATAAGCTTCTCAGTAGAAATTGTGT 57.145 30.769 0.00 0.00 41.19 3.72
1517 6750 9.944376 ATAAGCTTCTCAGTAGAAATTGTGTTA 57.056 29.630 0.00 0.00 41.19 2.41
1518 6751 8.854614 AAGCTTCTCAGTAGAAATTGTGTTAT 57.145 30.769 0.00 0.00 41.19 1.89
1519 6752 8.485976 AGCTTCTCAGTAGAAATTGTGTTATC 57.514 34.615 0.00 0.00 41.19 1.75
1521 6754 7.275779 GCTTCTCAGTAGAAATTGTGTTATCGA 59.724 37.037 0.00 0.00 41.19 3.59
1522 6755 9.140286 CTTCTCAGTAGAAATTGTGTTATCGAA 57.860 33.333 0.00 0.00 41.19 3.71
1530 6763 5.880054 AATTGTGTTATCGAACCTCCTTG 57.120 39.130 0.00 0.00 34.38 3.61
1535 6770 4.571176 GTGTTATCGAACCTCCTTGATTCC 59.429 45.833 0.00 0.00 34.38 3.01
1536 6771 4.469945 TGTTATCGAACCTCCTTGATTCCT 59.530 41.667 0.00 0.00 34.38 3.36
1627 7029 5.551233 TCTGTGAAAATCAGGAGTTCGATT 58.449 37.500 0.00 0.00 33.27 3.34
1628 7030 5.639506 TCTGTGAAAATCAGGAGTTCGATTC 59.360 40.000 0.00 0.00 30.64 2.52
1629 7031 4.388773 TGTGAAAATCAGGAGTTCGATTCG 59.611 41.667 0.00 0.00 30.64 3.34
1630 7032 4.625742 GTGAAAATCAGGAGTTCGATTCGA 59.374 41.667 4.29 4.29 30.64 3.71
1631 7033 5.292101 GTGAAAATCAGGAGTTCGATTCGAT 59.708 40.000 9.96 0.00 35.23 3.59
1741 7843 7.984050 TGGAGAAAACATCTGAAGATCTACATC 59.016 37.037 0.00 0.00 38.96 3.06
1742 7844 7.984050 GGAGAAAACATCTGAAGATCTACATCA 59.016 37.037 0.00 0.00 38.96 3.07
1833 7940 1.742411 CGTGACCCAATTAGATGGCGT 60.742 52.381 0.00 0.00 39.26 5.68
1844 7951 4.659111 TTAGATGGCGTAAATCGAAGGA 57.341 40.909 0.00 0.00 42.86 3.36
1857 7974 3.057969 TCGAAGGATTGATGTTGCTGT 57.942 42.857 0.00 0.00 0.00 4.40
1858 7975 3.411446 TCGAAGGATTGATGTTGCTGTT 58.589 40.909 0.00 0.00 0.00 3.16
1859 7976 4.574892 TCGAAGGATTGATGTTGCTGTTA 58.425 39.130 0.00 0.00 0.00 2.41
1860 7977 4.391830 TCGAAGGATTGATGTTGCTGTTAC 59.608 41.667 0.00 0.00 0.00 2.50
1861 7978 4.154015 CGAAGGATTGATGTTGCTGTTACA 59.846 41.667 0.00 0.00 0.00 2.41
1862 7979 5.334802 CGAAGGATTGATGTTGCTGTTACAA 60.335 40.000 0.00 0.00 0.00 2.41
1881 7998 8.426489 TGTTACAACTTACAACTCAGAATAGGT 58.574 33.333 0.00 0.00 0.00 3.08
1907 8029 7.772757 TGATTTTTATTTGTCTGTTTGCCCTTT 59.227 29.630 0.00 0.00 0.00 3.11
2041 8172 3.562635 GTTCCTTCCGAACTGCCG 58.437 61.111 0.00 0.00 46.33 5.69
2095 8235 3.550678 GGTAAGTCGTATTTTCTCTGCCG 59.449 47.826 0.00 0.00 0.00 5.69
2152 8292 9.264782 GCATTGTGTTTTGAATATGCAAATTAC 57.735 29.630 9.75 11.69 37.57 1.89
2222 8371 4.679654 GCTTTTAACCCTGATGTTTTGTCG 59.320 41.667 0.00 0.00 0.00 4.35
2239 8388 1.549170 GTCGGTAGGTCACAGGAACAT 59.451 52.381 0.00 0.00 31.21 2.71
2271 8420 3.503363 GCGTGTGGATCAGCAGCC 61.503 66.667 0.00 0.00 0.00 4.85
2295 8454 3.077359 CACCACTCTCCTTTCCAATGAC 58.923 50.000 0.00 0.00 0.00 3.06
2299 8458 4.006319 CACTCTCCTTTCCAATGACTTCC 58.994 47.826 0.00 0.00 0.00 3.46
2343 8502 1.734465 GCAAGCTTCATGAACGCTACT 59.266 47.619 23.68 12.60 32.90 2.57
2436 8595 6.081049 CCGAATACAAAAATCGTAGTTTGCA 58.919 36.000 7.16 0.00 38.10 4.08
2460 8631 1.004745 AGTTTGCACAATCCGATCCCT 59.995 47.619 0.00 0.00 0.00 4.20
2469 8641 4.158394 CACAATCCGATCCCTTTTTGTGAT 59.842 41.667 7.61 0.00 44.01 3.06
2480 8652 4.342092 CCCTTTTTGTGATCAACTTGGACT 59.658 41.667 0.00 0.00 32.93 3.85
2495 8667 1.204704 TGGACTCATTGACCGTAGCAG 59.795 52.381 0.00 0.00 33.17 4.24
2497 8669 2.480416 GGACTCATTGACCGTAGCAGAG 60.480 54.545 0.00 0.00 0.00 3.35
2509 8689 4.515944 ACCGTAGCAGAGCTAACTATAGTG 59.484 45.833 6.06 0.00 43.07 2.74
2511 8691 5.008811 CCGTAGCAGAGCTAACTATAGTGTT 59.991 44.000 6.06 0.00 43.07 3.32
2604 8806 4.019792 TGTGCTGCTCTGGATTTTTCTA 57.980 40.909 0.00 0.00 0.00 2.10
2705 8913 2.464157 ACTTGTGTAGAGCTCAAGGC 57.536 50.000 17.77 3.99 46.94 4.35
2801 9437 1.267882 CGCTCACTTAGTACGATCGCA 60.268 52.381 16.60 0.00 0.00 5.10
2803 9439 3.176708 GCTCACTTAGTACGATCGCAAA 58.823 45.455 16.60 3.50 0.00 3.68
2887 9526 8.736244 GTTTCTGAAGTATGAACTAGAGACTCT 58.264 37.037 10.47 10.47 33.75 3.24
2943 9584 1.028905 TTGCACCCGAACAAAAGAGG 58.971 50.000 0.00 0.00 0.00 3.69
2953 9596 5.449177 CCCGAACAAAAGAGGATGCTTATTC 60.449 44.000 0.00 0.00 0.00 1.75
3041 10954 8.040132 AGCTAGCATCCTCATAATTCTTCATAC 58.960 37.037 18.83 0.00 0.00 2.39
3085 11027 6.915300 TGGAACAACAAGTTTTCATGTAATCG 59.085 34.615 0.00 0.00 41.51 3.34
3088 11030 7.259290 ACAACAAGTTTTCATGTAATCGTCT 57.741 32.000 0.00 0.00 31.23 4.18
3119 11061 0.629058 ACCACAGGTTGTTTGGGAGT 59.371 50.000 0.00 0.00 34.41 3.85
3248 11196 4.154015 TCACTTGCGGTAAAGAATGTCATG 59.846 41.667 0.00 0.00 0.00 3.07
3326 11493 1.442148 GGCCTCGTCGCTTCCTTAT 59.558 57.895 0.00 0.00 0.00 1.73
3377 11565 5.883685 TCTCTCATACAGCCATTCAGAAT 57.116 39.130 0.00 0.00 0.00 2.40
3379 11567 6.053650 TCTCTCATACAGCCATTCAGAATTG 58.946 40.000 0.00 0.00 0.00 2.32
3380 11568 4.577693 TCTCATACAGCCATTCAGAATTGC 59.422 41.667 10.63 10.63 0.00 3.56
3383 11571 2.522185 ACAGCCATTCAGAATTGCAGT 58.478 42.857 18.84 14.68 32.34 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 10 5.409211 TCGCCGTATATTGAAGTGTTGTAA 58.591 37.500 0.00 0.00 0.00 2.41
25 27 0.031449 CCCACAAAAATGTTCGCCGT 59.969 50.000 0.00 0.00 0.00 5.68
159 165 9.620660 GTTAAAAAGTCCCACATGTAGTTAATG 57.379 33.333 0.00 0.00 0.00 1.90
160 166 9.357161 TGTTAAAAAGTCCCACATGTAGTTAAT 57.643 29.630 0.00 0.00 0.00 1.40
165 171 6.627395 TGTGTTAAAAAGTCCCACATGTAG 57.373 37.500 0.00 0.00 31.55 2.74
170 176 7.825331 TTATGATGTGTTAAAAAGTCCCACA 57.175 32.000 0.00 0.00 40.02 4.17
271 280 6.530181 CCTATTTCTAAATTTGTCCAAACGGC 59.470 38.462 0.00 0.00 32.51 5.68
272 281 6.530181 GCCTATTTCTAAATTTGTCCAAACGG 59.470 38.462 0.00 1.41 32.51 4.44
325 338 7.986320 TGCATCATCCATTTTCGGAAATAAAAT 59.014 29.630 0.16 0.00 38.95 1.82
342 355 5.319232 CGCATTTAAAATGTGCATCATCC 57.681 39.130 11.65 0.00 38.75 3.51
418 475 9.823098 TTCAAATATTGTGCATTTAAAACATGC 57.177 25.926 5.50 5.50 46.25 4.06
455 513 5.373222 TGTACAGTTCAAACATTGCCTACT 58.627 37.500 0.00 0.00 0.00 2.57
459 517 7.436673 TGTTAATTGTACAGTTCAAACATTGCC 59.563 33.333 6.91 0.00 0.00 4.52
460 518 8.346476 TGTTAATTGTACAGTTCAAACATTGC 57.654 30.769 6.91 0.00 0.00 3.56
578 639 1.514983 ATCATCCACTCTGCCCATCA 58.485 50.000 0.00 0.00 0.00 3.07
581 642 3.114606 TCTTTATCATCCACTCTGCCCA 58.885 45.455 0.00 0.00 0.00 5.36
582 643 3.471680 GTCTTTATCATCCACTCTGCCC 58.528 50.000 0.00 0.00 0.00 5.36
587 648 5.250235 TGAGACGTCTTTATCATCCACTC 57.750 43.478 21.08 2.50 0.00 3.51
609 670 3.070018 GCAACATGAAGCCGCTATCTAT 58.930 45.455 0.00 0.00 0.00 1.98
624 685 2.713967 GCCGGCCTCATTGCAACAT 61.714 57.895 18.11 0.00 0.00 2.71
696 1909 4.748600 CACCGAGTAGTGTATCGTCTATGA 59.251 45.833 0.00 0.00 37.23 2.15
790 2010 2.115266 CCCACAGACCCCACAACC 59.885 66.667 0.00 0.00 0.00 3.77
791 2011 2.115266 CCCCACAGACCCCACAAC 59.885 66.667 0.00 0.00 0.00 3.32
792 2012 2.369015 ACCCCACAGACCCCACAA 60.369 61.111 0.00 0.00 0.00 3.33
794 2014 4.660938 GCACCCCACAGACCCCAC 62.661 72.222 0.00 0.00 0.00 4.61
869 5845 1.210967 CGGAGAGTCTGAGTCTACCCT 59.789 57.143 17.17 0.00 0.00 4.34
870 5846 1.670791 CGGAGAGTCTGAGTCTACCC 58.329 60.000 17.17 12.95 0.00 3.69
871 5847 1.670791 CCGGAGAGTCTGAGTCTACC 58.329 60.000 17.17 16.14 0.00 3.18
872 5848 1.018910 GCCGGAGAGTCTGAGTCTAC 58.981 60.000 14.73 14.23 0.00 2.59
873 5849 0.913205 AGCCGGAGAGTCTGAGTCTA 59.087 55.000 14.73 0.00 0.00 2.59
877 5853 2.477176 CGGAGCCGGAGAGTCTGAG 61.477 68.421 5.05 0.00 35.56 3.35
993 6157 0.390340 TGAAGTGCAGCATCGTCTCC 60.390 55.000 0.00 0.00 0.00 3.71
1288 6491 3.870538 TCCATCATCCATCCAAGAAGG 57.129 47.619 0.00 0.00 39.47 3.46
1290 6493 3.723154 TCCATCCATCATCCATCCAAGAA 59.277 43.478 0.00 0.00 0.00 2.52
1291 6494 3.329277 TCCATCCATCATCCATCCAAGA 58.671 45.455 0.00 0.00 0.00 3.02
1292 6495 3.801307 TCCATCCATCATCCATCCAAG 57.199 47.619 0.00 0.00 0.00 3.61
1294 6497 2.310647 CCATCCATCCATCATCCATCCA 59.689 50.000 0.00 0.00 0.00 3.41
1295 6498 2.357881 CCCATCCATCCATCATCCATCC 60.358 54.545 0.00 0.00 0.00 3.51
1296 6499 2.949054 GCCCATCCATCCATCATCCATC 60.949 54.545 0.00 0.00 0.00 3.51
1297 6500 1.006758 GCCCATCCATCCATCATCCAT 59.993 52.381 0.00 0.00 0.00 3.41
1298 6501 0.406750 GCCCATCCATCCATCATCCA 59.593 55.000 0.00 0.00 0.00 3.41
1299 6502 0.324091 GGCCCATCCATCCATCATCC 60.324 60.000 0.00 0.00 34.01 3.51
1300 6503 0.679002 CGGCCCATCCATCCATCATC 60.679 60.000 0.00 0.00 34.01 2.92
1301 6504 1.381463 CGGCCCATCCATCCATCAT 59.619 57.895 0.00 0.00 34.01 2.45
1302 6505 2.832778 CCGGCCCATCCATCCATCA 61.833 63.158 0.00 0.00 34.01 3.07
1331 6534 1.002274 GCTGAGAAGGGAGGGGAGA 59.998 63.158 0.00 0.00 0.00 3.71
1339 6542 5.718724 AAGAAGAAAATTGCTGAGAAGGG 57.281 39.130 0.00 0.00 0.00 3.95
1340 6543 6.656693 TCCTAAGAAGAAAATTGCTGAGAAGG 59.343 38.462 0.00 0.00 0.00 3.46
1384 6600 2.359230 GACAGAGCCACAGCCCAC 60.359 66.667 0.00 0.00 41.25 4.61
1385 6601 4.007644 CGACAGAGCCACAGCCCA 62.008 66.667 0.00 0.00 41.25 5.36
1386 6602 3.941657 GACGACAGAGCCACAGCCC 62.942 68.421 0.00 0.00 41.25 5.19
1387 6603 2.433318 GACGACAGAGCCACAGCC 60.433 66.667 0.00 0.00 41.25 4.85
1389 6605 0.946221 GTTGGACGACAGAGCCACAG 60.946 60.000 0.00 0.00 0.00 3.66
1390 6606 1.069090 GTTGGACGACAGAGCCACA 59.931 57.895 0.00 0.00 0.00 4.17
1391 6607 1.668151 GGTTGGACGACAGAGCCAC 60.668 63.158 0.00 0.00 0.00 5.01
1392 6608 1.691195 TTGGTTGGACGACAGAGCCA 61.691 55.000 0.00 0.00 0.00 4.75
1393 6609 0.321653 ATTGGTTGGACGACAGAGCC 60.322 55.000 0.00 0.00 0.00 4.70
1394 6610 1.523758 AATTGGTTGGACGACAGAGC 58.476 50.000 0.00 0.00 0.00 4.09
1395 6611 3.563808 TGAAAATTGGTTGGACGACAGAG 59.436 43.478 0.00 0.00 0.00 3.35
1396 6612 3.546724 TGAAAATTGGTTGGACGACAGA 58.453 40.909 0.00 0.00 0.00 3.41
1415 6631 7.094162 GGCAGATGTAGATGTAGCTATAACTGA 60.094 40.741 10.04 0.00 35.71 3.41
1455 6686 3.888930 GAGGGACACTGAAATTGGTCAAA 59.111 43.478 0.00 0.00 32.00 2.69
1459 6690 2.982488 AGAGAGGGACACTGAAATTGGT 59.018 45.455 0.00 0.00 0.00 3.67
1474 6707 5.609423 AGCTTATTATGTCTTGCAGAGAGG 58.391 41.667 0.00 0.00 34.31 3.69
1478 6711 6.643388 TGAGAAGCTTATTATGTCTTGCAGA 58.357 36.000 0.00 0.00 0.00 4.26
1490 6723 8.854614 ACACAATTTCTACTGAGAAGCTTATT 57.145 30.769 0.00 0.00 42.66 1.40
1491 6724 8.854614 AACACAATTTCTACTGAGAAGCTTAT 57.145 30.769 0.00 0.00 42.66 1.73
1492 6725 9.944376 ATAACACAATTTCTACTGAGAAGCTTA 57.056 29.630 0.00 0.00 42.66 3.09
1493 6726 8.854614 ATAACACAATTTCTACTGAGAAGCTT 57.145 30.769 0.00 0.00 42.66 3.74
1496 6729 8.689251 TCGATAACACAATTTCTACTGAGAAG 57.311 34.615 0.00 0.00 42.66 2.85
1500 6733 7.383687 AGGTTCGATAACACAATTTCTACTGA 58.616 34.615 0.00 0.00 37.34 3.41
1506 6739 6.148811 TCAAGGAGGTTCGATAACACAATTTC 59.851 38.462 0.00 0.00 37.34 2.17
1512 6745 4.571176 GGAATCAAGGAGGTTCGATAACAC 59.429 45.833 0.00 0.00 37.34 3.32
1514 6747 4.811557 CAGGAATCAAGGAGGTTCGATAAC 59.188 45.833 0.00 0.00 34.66 1.89
1515 6748 4.469945 ACAGGAATCAAGGAGGTTCGATAA 59.530 41.667 0.00 0.00 0.00 1.75
1517 6750 2.840651 ACAGGAATCAAGGAGGTTCGAT 59.159 45.455 0.00 0.00 0.00 3.59
1518 6751 2.257207 ACAGGAATCAAGGAGGTTCGA 58.743 47.619 0.00 0.00 0.00 3.71
1519 6752 2.770164 ACAGGAATCAAGGAGGTTCG 57.230 50.000 0.00 0.00 0.00 3.95
1521 6754 3.170717 TCGTACAGGAATCAAGGAGGTT 58.829 45.455 0.00 0.00 0.00 3.50
1522 6755 2.816411 TCGTACAGGAATCAAGGAGGT 58.184 47.619 0.00 0.00 0.00 3.85
1530 6763 5.461526 TGATCATCGAATCGTACAGGAATC 58.538 41.667 1.52 0.00 0.00 2.52
1535 6770 4.233005 AGCATGATCATCGAATCGTACAG 58.767 43.478 4.86 0.00 0.00 2.74
1536 6771 4.229876 GAGCATGATCATCGAATCGTACA 58.770 43.478 4.86 0.00 0.00 2.90
1627 7029 0.932399 CATGCGCATGTGAAGATCGA 59.068 50.000 36.45 0.00 34.23 3.59
1628 7030 0.041576 CCATGCGCATGTGAAGATCG 60.042 55.000 39.70 23.06 37.11 3.69
1629 7031 1.003116 GTCCATGCGCATGTGAAGATC 60.003 52.381 39.70 23.15 37.11 2.75
1630 7032 1.019673 GTCCATGCGCATGTGAAGAT 58.980 50.000 39.70 9.94 37.11 2.40
1631 7033 0.321475 TGTCCATGCGCATGTGAAGA 60.321 50.000 39.70 29.35 37.11 2.87
1689 7791 5.242393 GGAAGGAAATGTATGCTATGCACAT 59.758 40.000 0.00 0.00 43.04 3.21
1741 7843 1.623811 ACTGTACTACCCCAGCACTTG 59.376 52.381 0.00 0.00 31.76 3.16
1742 7844 2.025636 ACTGTACTACCCCAGCACTT 57.974 50.000 0.00 0.00 31.76 3.16
1833 7940 5.647658 ACAGCAACATCAATCCTTCGATTTA 59.352 36.000 0.00 0.00 36.54 1.40
1857 7974 8.644216 TCACCTATTCTGAGTTGTAAGTTGTAA 58.356 33.333 0.00 0.00 0.00 2.41
1858 7975 8.185506 TCACCTATTCTGAGTTGTAAGTTGTA 57.814 34.615 0.00 0.00 0.00 2.41
1859 7976 7.062749 TCACCTATTCTGAGTTGTAAGTTGT 57.937 36.000 0.00 0.00 0.00 3.32
1860 7977 8.553459 AATCACCTATTCTGAGTTGTAAGTTG 57.447 34.615 0.00 0.00 0.00 3.16
1861 7978 9.574516 AAAATCACCTATTCTGAGTTGTAAGTT 57.425 29.630 0.00 0.00 0.00 2.66
1862 7979 9.574516 AAAAATCACCTATTCTGAGTTGTAAGT 57.425 29.630 0.00 0.00 0.00 2.24
1881 7998 6.825610 AGGGCAAACAGACAAATAAAAATCA 58.174 32.000 0.00 0.00 0.00 2.57
1895 8012 5.010012 AGTTCATCTACAAAAGGGCAAACAG 59.990 40.000 0.00 0.00 0.00 3.16
1931 8057 3.232213 CTACGAGGTAGCTGCTCAAAA 57.768 47.619 4.91 0.00 29.12 2.44
2041 8172 1.312815 GCAAGTATGATGACAGCCCC 58.687 55.000 0.00 0.00 0.00 5.80
2095 8235 3.194861 GGGTTGTTGTTTTTCTTGAGGC 58.805 45.455 0.00 0.00 0.00 4.70
2153 8293 9.823647 GGAGAAAGAAAGATACACATGATCTTA 57.176 33.333 0.00 0.00 41.71 2.10
2154 8294 8.547173 AGGAGAAAGAAAGATACACATGATCTT 58.453 33.333 0.00 0.49 43.88 2.40
2155 8295 8.088463 AGGAGAAAGAAAGATACACATGATCT 57.912 34.615 0.00 0.00 35.08 2.75
2222 8371 3.695830 TCAATGTTCCTGTGACCTACC 57.304 47.619 0.00 0.00 0.00 3.18
2239 8388 1.150827 CACGCTGCACTGAAGATCAA 58.849 50.000 0.00 0.00 0.00 2.57
2271 8420 3.423539 TTGGAAAGGAGAGTGGTGATG 57.576 47.619 0.00 0.00 0.00 3.07
2343 8502 0.251474 AGCTCAAGAAAGCCATGGCA 60.251 50.000 37.18 14.88 43.56 4.92
2436 8595 1.317613 TCGGATTGTGCAAACTGCTT 58.682 45.000 0.00 0.00 45.31 3.91
2447 8618 3.761897 TCACAAAAAGGGATCGGATTGT 58.238 40.909 0.00 0.00 0.00 2.71
2460 8631 6.713762 ATGAGTCCAAGTTGATCACAAAAA 57.286 33.333 3.87 0.00 37.77 1.94
2469 8641 2.104111 ACGGTCAATGAGTCCAAGTTGA 59.896 45.455 3.87 0.00 0.00 3.18
2480 8652 1.186200 AGCTCTGCTACGGTCAATGA 58.814 50.000 0.00 0.00 36.99 2.57
2495 8667 4.823989 TCCCGGTAACACTATAGTTAGCTC 59.176 45.833 1.56 0.00 45.47 4.09
2497 8669 5.520376 TTCCCGGTAACACTATAGTTAGC 57.480 43.478 1.56 3.33 44.68 3.09
2509 8689 0.392060 ATCCGTTGCTTCCCGGTAAC 60.392 55.000 0.00 0.00 44.51 2.50
2511 8691 1.219664 CATCCGTTGCTTCCCGGTA 59.780 57.895 0.00 0.00 44.51 4.02
2604 8806 9.041354 AGAAGTCATACTATCCTCAAAAGAAGT 57.959 33.333 0.00 0.00 0.00 3.01
2755 8967 9.432982 GATCTCCTGACCTAAGATCCATATATT 57.567 37.037 0.00 0.00 39.56 1.28
2839 9475 3.356529 AATTAAGGTGGCCAGACTCTG 57.643 47.619 5.11 0.00 0.00 3.35
2843 9482 5.123979 CAGAAACTAATTAAGGTGGCCAGAC 59.876 44.000 5.11 1.34 0.00 3.51
2887 9526 5.199723 TCAGGGTGCAAAATGATTATGCTA 58.800 37.500 0.00 0.00 40.66 3.49
2898 9537 2.199652 CCGGCTTCAGGGTGCAAAA 61.200 57.895 0.00 0.00 0.00 2.44
2932 9573 8.816640 TTTTGAATAAGCATCCTCTTTTGTTC 57.183 30.769 0.00 0.00 0.00 3.18
2962 9605 4.994907 AAAGTACGCCCTGTTTCTTTTT 57.005 36.364 0.00 0.00 33.13 1.94
2964 9607 6.002082 AGAATAAAGTACGCCCTGTTTCTTT 58.998 36.000 0.00 0.00 37.34 2.52
2965 9608 5.557866 AGAATAAAGTACGCCCTGTTTCTT 58.442 37.500 0.00 0.00 0.00 2.52
2967 9610 5.410439 TCAAGAATAAAGTACGCCCTGTTTC 59.590 40.000 0.00 0.00 0.00 2.78
2969 9612 4.901868 TCAAGAATAAAGTACGCCCTGTT 58.098 39.130 0.00 0.00 0.00 3.16
2970 9613 4.546829 TCAAGAATAAAGTACGCCCTGT 57.453 40.909 0.00 0.00 0.00 4.00
2971 9614 5.584649 TCAATCAAGAATAAAGTACGCCCTG 59.415 40.000 0.00 0.00 0.00 4.45
2972 9615 5.741011 TCAATCAAGAATAAAGTACGCCCT 58.259 37.500 0.00 0.00 0.00 5.19
2973 9616 6.430451 CATCAATCAAGAATAAAGTACGCCC 58.570 40.000 0.00 0.00 0.00 6.13
2974 9617 5.909610 GCATCAATCAAGAATAAAGTACGCC 59.090 40.000 0.00 0.00 0.00 5.68
2975 9618 6.486248 TGCATCAATCAAGAATAAAGTACGC 58.514 36.000 0.00 0.00 0.00 4.42
2976 9619 8.894409 TTTGCATCAATCAAGAATAAAGTACG 57.106 30.769 0.00 0.00 0.00 3.67
3060 10973 6.915300 CGATTACATGAAAACTTGTTGTTCCA 59.085 34.615 0.00 0.00 38.03 3.53
3085 11027 5.608449 ACCTGTGGTTACTTCTGTTAAGAC 58.392 41.667 0.00 0.00 27.29 3.01
3088 11030 5.747342 ACAACCTGTGGTTACTTCTGTTAA 58.253 37.500 1.34 0.00 45.01 2.01
3119 11061 2.352421 GGTTTGTGCGTCTGCTACTCTA 60.352 50.000 0.00 0.00 43.34 2.43
3194 11142 3.254827 TGAGTTCGCTCGATCGATAAG 57.745 47.619 19.78 12.74 46.95 1.73
3197 11145 1.335182 ACATGAGTTCGCTCGATCGAT 59.665 47.619 19.78 1.60 46.95 3.59
3265 11213 0.037326 GCCCTTGCTTTTACCTTGCC 60.037 55.000 0.00 0.00 33.53 4.52
3271 11219 2.504026 GCGCGCCCTTGCTTTTAC 60.504 61.111 23.24 0.00 34.43 2.01
3298 11246 2.665185 ACGAGGCCGACTTGCAAC 60.665 61.111 0.00 0.00 39.50 4.17
3326 11493 1.003580 GGAGACCTTGTCATGCAGGAA 59.996 52.381 0.92 0.00 34.60 3.36
3379 11567 9.516314 ACAAGTTCTTTTATCTTTTGTAACTGC 57.484 29.630 0.00 0.00 0.00 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.